GEDI: Gene expression decomposition and integration

Content

• Overview
• Requirements
• Installation
• Usage
• License
• Article
• Reproducible analysis for manuscript
• Contact

Overview

A generative model that unifies integration, cluster-free differential expression, pathway and regulatory network analysis, data normalization and imputation.

Requirements

The following R packages are required:

• Rcpp
• RcppEigen
• ggplot2
• metR
• rsvd
• scales

Note, RcppEigen also needs gfortran to be installed on the system.

Other R dependencies (used for the notebooks):

• uwot
• scran
• scater

The code was tested using R 4.0.0 running on CentOS Linux 7.

GEDI should be compatible with Windows, Mac, and Linux operating systems.

Installation

From an R session, type:

devtools::install_github("csglab/GEDI")

Usage

Check the following notebooks for examples on how to run GEDI:

• Quick intro
• Analysis of sample to sample variability
• TF analysis in PBMC
• Ratio mode: splicing

Article

Madrigal, A., Lu, T., Soto, L. M., & Najafabadi, H. S. (2024). A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data. Nature Communications, 15(1), 6573.

Contact

We use GitHub issues for tracking requests and bugs. Please submit a new issue if you have any comment or you would like to report a software bug.